Lukas Heumos

> Maybe there's even room for a dedicated package for DE visualizations thinking It could go into https://github.com/theislab/pertpy/ but I'm not sure whether I'd like adding plotting functions without having...

It's currently being rewritten, but it's not something that I consider stable or maintained enough to be used for this purpose.

> RE pertpy: I'm not quite sure I understood the scope of that package. If DE methods are not the scope of this package, it indeed feels a bit weird...

> > However, we don't want to reimplement DE methods because doing that well is a project itself (see diffxpy or the recent pydeseq2 attempts). > > Ok, but maybe...

So take away from this issue is: More decoupler - yes. More/better visualizations - yes, but we'll implement them externally first and then add them to the DE notebook. Thank...

Excellent idea. What is the easiest solution for this? Some of these? https://stackoverflow.com/questions/49429585/how-to-change-the-background-color-of-a-single-cell-in-a-jupyter-notebook-jupy Seem a bit annoying to use in every notebook...

Follow discussion https://discourse.pangeo.io/t/statement-of-need-integrating-jupyterbook-and-jupyterhubs-via-ci/2705

> @Zethson I don't think you have decided how to handle datasets yet? I'll leave that until we know what the solution is. Not finally at least.That's fine with me....

Merging notebooks is always hell. I think it would be easiest for me if you merge Malte's text into your notebook and we merge yours.

Hey, great timing! @ivirshup is currently already on this with this PR :) https://github.com/theislab/single-cell-best-practices/pull/119 Maybe the two of you can coordinate?